computer modeling in molecular biology.pdf

4 Molecular Dynamics and Free Energy Calculations 79(a) Average number of hydrogenbonds made by thesidechain of each residuewith backbone atoms.(b) Average number of hydrogenbonds made by thesidechain of each residuewith other sidechains.3.0 1 n2.01.0(c) Average number of hydrogenbonds made by thesidechain of each residue0 10 20 30 40 50 60 70 80 90 100 110 N with water molecules.(c)Figure 4-11. The average number of hydrogen bonds formed by individual residues along thesequence during the 250 ps molecular dynamics simulation of barnase in water.In each case the average number of the corresponding hydrogen bonds is computed by summingthe average number of hydrogen bonds, defined as in legend of Figure 4-10, made by alldonor and acceptor groups of the sidechain and dividing it by the number of donors and acceptorsin the sidechain.